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Ion Torrent machine ushers in a new era of sequencing

It’s not much bigger than a breadbox, yet it opens up a new way of analyzing the individual “letters” in DNA. Wrapped in a pastel plastic case, powered by silicon chips that are common all over the world, the Ion Torrent Personal Genome Machine is finally being released commercially.

But this genetic sequencing technology is no stranger to the Broad. Chad Nusbaum, Niall Lennon, and their colleagues at the Broad's 320 Charles Street location have been putting three Ion Torrents through their paces for awhile now. I got a chance to watch them kick the tires.

The tests, done in collaboration with Ion Torrent Systems in Connecticut, were designed “to optimize the machine and get it ready for when it will actually go out into the wide world and others will use it,” Niall, assistant director of the Broad’s Genome Sequencing Platform, told me as he showed me the iPod controller, complete with apps. The three machines were busy analyzing, or sequencing, the DNA of model organisms like the bacterium E. coli in order to assess performance. Because biologists are so familiar with the genetic sequence of E. coli’s DNA, they are able to spot errors easily and see how the machines measure up.

The Ion Torrent test run was just one example of the Broad’s partnerships with companies building new sequencing machines. Broad scientists in the Genome Sequencing and Analysis Program, along with others, serve as early-access users who share feedback and suggest tweaks as new technology is developed.

What has made the Ion Torrent newsworthy? Chad, co-director of the Genome Sequencing and Analysis Program, calls it the “first post-light technology.” By that, he means the fact that the Ion Torrent machine eliminates the need for expensive light-sensing optics and, instead, relies on detecting a chemical reaction that is “written” electronically onto a silicon chip.

And it’s the “post-light” part of the Ion Torrent technology that has sparked curiosity. (In genetic sequencers commonly used today, the individual DNA “letters,” known as nucleotides, are labeled with a fluorescent material. Sequencers shine a laser onto a template containing the labeled “letters” and read the fluorescent signals.) The Ion Torrent machine eliminates the labels, lasers, and camera equipment used to read the genetic data. When an individual “letter” bonds with a growing strand of DNA that scientists are examining in the lab, a chemical reaction takes place, releasing a positively charged hydrogen ion. The silicon chip in the Ion Torrent chip measures the resulting negative pH change, which sends a charge to a sensing layer underneath tiny “wells” that have been machined onto the chip. That pH change is turned into voltage, which can be measured.

Because the machine uses silicon chips – which seem ubiquitous enough to power our entire lives – and does not have expensive lasers or lenses, it can work faster and cost less.

It has even sparked a new contest. Life Technologies, which acquired Ion Torrent in October, has announced a $7 million contest, inviting researchers to churn out data ever faster. There will be seven Life Grand Challenges in all. The judges for the first three include Jonathan Rothberg, the machine’s inventor, and two Nobel laureates in chemistry. Check out the details here.

Chad is quoted by Forbes.com blogger Matthew Herper in an online piece that can be found here.